77 Open source projects that are alternatives of or similar to SCope

R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

Inference of switch-like differential expression along single-cell trajectories

Manuscript for functional prediction of transcriptomic “dark matter” across species

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

No description or website provided.

Methods for detecting doublets in single-cell sequencing data

Interactive R package to quantify, analyse and visualise alternative splicing

Spatial alignment of single cell transcriptomic data.

Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

Data and code related to the paper "ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa..." Jie Tan, et al · mSystems · 2016

spatial transcriptome, single cell

Differential Gene Correlation Analysis

An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.

Multiome GRN inference.

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

This repository contains the tensorflow implementation of "GNE: A deep learning framework for gene network inference by aggregating biological information"

Non-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)

🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

A tool for semi-automatic cell type annotation

Reference mapping for single-cell genomics

GREIN : GEO RNA-seq Experiments Interactive Navigator

A fast, accurate, and modularized dimensionality reduction approach based on diffusion harmonics and graph layouts. Escalates to millions of samples on a personal laptop. Adds high-dimensional big data intrinsic structure to your clustering and data visualization workflow.

Make rapid visualizations of RNA-seq data in R

Papers with code for single cell related papers

Transcripts annotation and GO enrichment Fisher tests

Clone identification from single-cell data

💡 💾 💽 A simple, intuitive and Efficient single cell binary Data Storage format

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

mgatk: mitochondrial genome analysis toolkit

TCGA data acquisition and processing for Project Cognoma

Software for exploration of gene expression data from single-cell RNA sequencing.

kallisto | bustools workflow for pre-processing single-cell RNA-seq data

R API and htmlwidget for Vitessce

R package to access DoRothEA's regulons

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

Graph-linked unified embedding for single-cell multi-omics data integration

Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.

Experimental design framework for scRNAseq population studies (eQTL and DE)

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

Dynamical systems methods for RNA velocity analysis

VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps

📊 Gene expression in neuroexpresso database

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data

R package to do the Ligand Receptor Analysis Visualization

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

Bead-based single-cell atac processing

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

Deep learning model for single-cell inference of multi-omic profiles from a single input modality.